Then, put unbreakable teleporters (maybe two-ways teleporters) in each part for conect each others.
I like your idea. But if you use two-way teleporters, how would the player be able to visit more than 2 sub-maps? Put multiple 'porters in each section?
What if those special teleporters also teleported ammo rounds fired at them? So I could, like, flee a Baron of Hell through the teleporter, and then fire through it back at the Baron?
I think it's not a very good idea. Even if the situation presented itself, the to-hit penalty for firing out of LOS would be too great for players to use this strategically. Also, applying the technique would be cheatish, like giftdropping and attacking out of LOS in previous versions.
But if the flying ammo were teleported it would drop on the other teleporter because it can not teleport the movement of the ammo.
Oh, how I hate applying real world physics to a fictional environment. ;) Even though you're strictly right, implementing teleportation of a moving subject in a game would be no problem at all.